Hi-C contact maps

The resources below support the paper “Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture” by Eitan Yaffe and Amos Tanay (Nature Genetics 2011), in which we develop a probabilistic model for Hi-C data and explore chromosomal architectures in human lymphoblasts using it.

Smooth normalized matrices (1Mb bins) for the Lieberman-Aiden et. al paper are given in HiC_maps_2011.tar.gz.

Hi-C Pipeline (hicpipe)

Hicpipe is a set of scripts and programs that correct Hi-C contact maps, given a list restriction enzyme sites and mapped paired reads. The latest version is hicpipe_0.93.tar.gz. Example input datasets (for the maps published in the Lieberman-Aiden et al. paper) can found in hicpipe_Lieberman2009.tar.gz. Previous hicpipe versions can be found here.

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